Faraday instability on a sphere: numerical simulation

We consider a spherical variant of the Faraday problem, in which a spherical drop is subjected to a time-periodic body force, as well as surface tension. We use a full three-dimensional parallel front-tracking code to calculate the interface motion of the parametrically forced oscillating viscous drop, as well as the velocity field inside and outside the drop. Forcing frequencies are chosen so as to excite spherical harmonic wavenumbers ranging from 1 to 6. We excite gravity waves for wavenumbers 1 and 2 and observe translational and oblate-prolate oscillation, respectively. For wavenumbers 3 to 6, we excite capillary waves and observe patterns analogous to the Platonic solids. For low viscosity, both subharmonic and harmonic responses are accessible. The patterns arising in each case are interpreted in the context of the theory of pattern formation with spherical symmetry

The ICON-1.2 hydrostatic atmospheric dynamical core on triangular grids – Part 1: Formulation and performance of the baseline version

Abstract. As part of a broader effort to develop next-generation models for numerical weather prediction and climate applications, a hydrostatic atmospheric dynamical core is developed as an intermediate step to evaluate a finite-difference discretization of the primitive equations on spherical icosahedral grids. Based on the need for mass-conserving discretizations for multi-resolution modelling as well as scalability and efficiency on massively parallel computing architectures, the dynamical core is built on triangular C-grids using relatively small discretization stencils. This paper presents the formulation and performance of the baseline version of the new dynamical core, focusing on properties of the numerical solutions in the setting of globally uniform resolution. Theoretical analysis reveals that the discrete divergence operator defined on a single triangular cell using the Gauss theorem is only first-order accurate, and introduces grid-scale noise to the discrete model. The noise can be suppressed by fourth-order hyper-diffusion of the horizontal wind field using a time-step and grid-size-dependent diffusion coefficient, at the expense of stronger damping than in the reference spectral model. A series of idealized tests of different complexity are performed. In the deterministic baroclinic wave test, solutions from the new dynamical core show the expected sensitivity to horizontal resolution, and converge to the reference solution at R2B6 (35 km grid spacing). In a dry climate test, the dynamical core correctly reproduces key features of the meridional heat and momentum transport by baroclinic eddies. In the aqua-planet simulations at 140 km resolution, the new model is able to reproduce the same equatorial wave propagation characteristics as in the reference spectral model, including the sensitivity of such characteristics to the meridional sea surface temperature profile. These results suggest that the triangular-C discretization provides a reasonable basis for further development. The main issues that need to be addressed are the grid-scale noise from the divergence operator which requires strong damping, and a phase error of the baroclinic wave at medium and low resolutions

Deep representations of structures in the 3D-world

This thesis demonstrates a collection of neural network tools that leverage the structures and symmetries of the 3D-world. We have explored various aspects of a vision system ranging from relative pose estimation to 3D-part decomposition from 2D images. For any vision system, it is crucially important to understand and to resolve visual ambiguities in 3D arising from imaging methods. This thesis has shown that leveraging prior knowledge about the structures and the symmetries of the 3D-world in neural network architectures brings about better representations for ambiguous situations. It helps solve problems which are inherently ill-posed

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response